[gmx-users] dummy atoms & timesteps
feenstra at chem.vu.nl
Wed Dec 18 12:38:29 CET 2002
J Simms wrote:
> Hi all,
> Qu1I am just reading Antons '99 paper re large time-scale. Are the
> dummy atoms produced by pdb2gmx implimented the same as in
> the paper, or are they different?
Yes - exact same thing. I implemented it myself in pdb2gmx
explicitly for this paper. There is a more recent addition
to dummify aromatic amino-acid sidechains also, but the
article wich contains the corresponding description did not get
past the referees:
K. Anton Feenstra, Herman J. C. Berendsen and Alan E. Mark Hierarchical
Motion in Small Proteins: Implications for Protein Folding .
> Qu2. Can I just let pdb2gmx get on with producing dummy atoms,
> or do I have to look & do anything ;-)
Yes - the implementation in pdb2gmx for -dummy hydrogens at least
is designed to be generic, although I haven't tested with explicit
> Qu3. When doing MD with dummy atoms, heavy hydrogens and a
> large timestep. What do I look for when comparing it with a smaller
> (ie 2fs) timestep & checking its right.
That basically depends on whatever properties you are interested
in. You could as a basic check look at e.g. rmsd values an so on.
I've used calculated NMR relaxation parameters as a comparison
(these are not trivial to calculate, and not implemented in one of
the Gromacs analysis tools) in one of my recent papers on trajectories
run at 2 (normal) and 4 and 7 fs timestep (w/ heavy&dummy):
K. Anton Feenstra, C. Peter*, Ruud M. Scheek, Alan E. Mark and Wilfred F.
van Gunsteren* A comparison of methods for calculating NMR
cross-relaxation rates (NOESY and ROESY intensities) in small peptides.
(2002) J. Biomol. NMR 23, 181-194.
* Laboratory of Physical Chemistry, Swiss Federal Institute of Technology
> Qu4. Are there other paper re increasing the timestep of MD?
See references in my paper. I haven't checked the more recent literature.
I hadn't found any whith something similar to my dummy constructions.
Most modified the hydrogen masses, but without compensating the total
system mass. I (i.e. the pdb2gmx implementation) shift the increased
hydrogen mass from the bonded heavy atom (i.e. the heavy atom gets lighter).
Increasing total system mass scales your overal time-scale!
One particularly bad one scaled the mass of *all* atoms in the system and
keeping *velocities* the same. That is equivalent to taking a larger
timestep (scales as sqrt(T_mass) ) and increasing temperature (which
derives from 1/2 m*v^2).
| | Anton Feenstra |
| . | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |---- | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands |
| |---- | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| ' __ | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
| / \ |-----------------------------------------------------------|
| ( ) | Dept. of Biophysical Chemistry - University of Groningen |
| \__/ | Nijenborgh 4 - 9747 AG Groningen - The Netherlands |
| __ | Tel +31 50 363 4327 - Fax +31 50 363 4800 |
| / \ | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton |
| ( ) |-----------------------------------------------------------|
| \__/ | "Three Little Fonzies" (Pulp Fiction) |
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